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Biomed > biomed week 1 and 2 > Flashcards

biomed week 1 and 2 Flashcards

1
Q

covalent bonds can be … and … in nature

A

polar and non polar

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2
Q

electronegativity is the …

A

affinity of an atom for electrons

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3
Q

what are the three factors electronegativity is determined by

A
  • protons in nucleus
    -distance electrons are from the nucleus
  • shielding of electrons from the nucleus
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4
Q

what does a difference in electronegativity of covalent bond forming atoms > 0.5 signify?

A

atom with higher electronegativity will attract more elctrons than the other

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5
Q

what are the three van de waals forces?

A

dipole - dipole (strongest)
dipole induced dipole
induced dipole - induced dipole (weakest)

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6
Q

what is an example of a dipole dipole interaction

A

H bonding

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7
Q

how do hydrophobic non covalent bonds interact in the cell membrane

A

cluster on the surface of the membrane proteins

and

cluster in the interior of soluble proteins

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8
Q

what are non covalent ionic interactions

A

attractions between oppositely charged molecules

when they occur between amino acid side chains of protiens, ionic bonds are reffered to as side bridges

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9
Q

functional groups are what form of bonding

A

non covalent bonding patterns based on their polarities

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10
Q

what is the reason that energy is released upon cleaving the phosphoryl group?

A

charges close together want to repeal, releasing energy

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11
Q

what are two things monosaccharides usually include?

A

minimum of three C’s
hydroxyl groups plus either an aldehyde or a ketone group

(generic naming is based on the number of carbons)

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12
Q

are monosaccarides linear or cyclic?

A

can be either

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13
Q

what kind of bonds do monosaccharides make to form disaccharides or polysaccharides?

A

glycosidic bonds

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14
Q

fatty acids attach to a gylcerol backbone to create a mono di or triglycerides using what kind of bond?

A

ester linkage

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15
Q

amino acids use what kind of bonds to be incorperated into protiens?

A

peptide bonds

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16
Q

what is the general structure of nucleotides

A

nitrogenous base ( purines - double ring structure, pyrimidines - single ring structure) , 5 carbon sugar and phosphate group(s)

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17
Q

nucleotides form nucleic acids via a ….. bond

A

phosphodiester

  • strongest covalent linkage
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18
Q

specific examples of oxireductases include

A

dehydrogenase and oxidases

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19
Q

what do dehydrogenases do?

A

remove Hs and donate them to a molecule other than oxygen

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20
Q

what do oxidases do?

A

remove Hs and donate them to oxygen

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21
Q

transferases

A

synthesize molecules by catalyzing the transfer group from one molecule to another

often use nucleophilic substitution

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22
Q

what are two specific transferases

A

kinases
- transfer a phosphate group from ATP to another non water molecule

polymerases
- transfers a monomer to a polymer especially wrt DNA and RNA

X transferases
- transfers “X” from one molecule to the other
- changes the ending of name of the group
being transfered to “ yl

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23
Q

what do hydrolases include

A

NUCLEOPHILIC SUBSTITUTION
catalyze hydrolysis reactions

phosphatases
- hydrolyse nonophosphate esters (AMP but not ATP) to release a phosphate group

ATPases
- hydrolyse ATP to release a phosphate group
- X ases where X refers to the molecule being
broken apart
- ex. peptidases hydrolyse peptides to
release smaller fragments

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24
Q

what are the three types of reactions catalysed by lyases?

A

addition
- adds one molecule to another across a 2X or
3X carbon bond
- hydratase
elimination
- removed atoms in a molecule to create a double bond
- dehydratases , decarboxylases

condensation
- synthase
- joins two molecules creating a C-C bond

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25
Q

what is the name of the reaction where ATP donates a phosphate

A

kinase

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26
Q

what is unique about lyases

A

they break down molecules without water

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26
Q

what is unique about a synthase

A

a synthase is a type of lyase that can break covalent bonds without the use of ATP

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26
Q

what enzyme often breaks a bond and forms a double bond

A

lyases

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27
Q

hydrolase versus hydratase
versus hydrolysis

A

hydrolase catalyzes an addition of a water molecule across a double bond
- phosphatases
- hydrolyse monophosphate esters

hydratase enzymes catalyse addition of water molecules , double bond gets converted to single bond

hydrolases catalyze hydrolysis reactions

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27
Q

decarboxylases is an example of what enzyme? and carboxylases are an example of what enzyme?

A

lyases
ligases

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27
Q

what are isomerases?

A

they switch isomerize (rearrange groups within a molecule)

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27
Q

what are the three types of isomerases

A

mutases
- transfer functional groups intramolecularly
epimerases
- interconvert the groups around an asymmetric carbon in a molecule that has more than one asymetrical carbon

racemases
- interconvert the groups around an asymetrical carbon in a molecule that only has one asmetrical carbon

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28
Q

what is the function of ligases

A

ligases create bonds between two molecules
with the use of an ATP molecule

“X ligases” and “X “ synthetases
- X refers to the name of the molecules being joined or the molecule being created

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29
Q

what is the first law of thermodynamics

A

energy in the universe is constant but energy forms will change

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30
Q

what is enthalpy?

A

the energy contents of the bonds within a system

we tend to measure this in change that occurs when reactants go to products

can be measured by heat change in a system

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31
Q

a reaction that releases heat is

A

exothermic negative H
tends to be spontanous

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32
Q

a reaction that absorbs heat is

A

endothermic positive H
tends to not be spontaneous but depends

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33
Q

what is the definition of entropy

A

how spread out or dispersed energy is in a system

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34
Q

increase in entropy means that the energy in the system is

A

more dispersed

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35
Q

what is the second law of thermodynamics

A

energy disperses or spreads out unless it is hindered from doing so

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36
Q

what does gibbs free energy

A

measures the energy difference between the products and reactants and takes into account both entropy and enthalpy

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37
Q

what is the gibbs free energy equation

A

triangleG = triangleH - TtriangleS

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38
Q

negative triangle G is

A

an exergonic reaction = spontaneous

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39
Q

positive triangle G is

A

an endergonic reaction = non spontaneous

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40
Q

gibbs free energy is dependant on

A

temperature, pH and relative concentrations of products and reactants

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41
Q

a negative triangleH will cause a more …

A

spontaneous reaction

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42
Q

a positive triangleS will cause a more …..

A

spontaneous reaction

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43
Q

a positive triangleH and a negative triangleS will …

A

never be spontaneous

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44
Q

non standard gibbs free energy is when

A

when both reactants and products are both not at 1M

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45
Q

gibbs free energy equation

A

triangleG =triangleG knot+ RT inverse log of products / reactants

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46
Q

how does gibbs free energy change when the reactants are increased compared to the products

A

triangleG becomes more negative, more likely to be exergonic

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47
Q

how does gibbs free energy change when the reactants are reduced compared to the products

A

more positive triangleG

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48
Q

even reactions with a positive triangleG can develop into exergonic reactions if the …. are substancially greater than the …..

A

reactants , products

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49
Q

gibbs free energy coupled reactions are

A

additive, sum of triangleG

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50
Q

the high energy phosphodiester bond , when broken, has a negative triangle G, that energy can be coupled with another reaction with a positive triangleG
the net reaction is …… if triangleG of ATP is negative enough to counteract endergonic triangle G of the coupled reaction

A

exergonic

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51
Q

why are NADH and FADH2 indirect energy

A

because they need to be oxidized in the mitochondria and they need to go to the ETC to make ATP

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52
Q

gluconeogenesis purpose and location

A

makes glucose from precursor molecules
mitochondria and cytosol

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53
Q

glycogenesis purpose and location

A

makes glycogen to store glucose
cytosol

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54
Q

fatty acid synthesis purpose and location

A

makes fatty acids from Acetyl CoA
cytosol

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55
Q

lipogenesis purpose and location

A

adds fatty acids to a glycerol backbone to make triglyceride lipids
cytosol

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56
Q

ketogenesis purpose and location

A

makes ketone bodies from acetyl CoA
mitochondria

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57
Q

pentose phosphate shunt purpose and location

A

shunts glucose into the creation of various 5 Carbon sugars and NADPH
cytosol

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58
Q

glycogenolysis purpose and location

A

breakdown of glycogen to release glucose. glucose can then enter glycolysis to produce energy
cytosol

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59
Q

glycolysis purpose and location

A

breakdown of glucose to pyruvate to produce energy (NADH and ATP) After glycolysis pyruvate can be converted to acetyl coA to enter the CAC to produce more energy

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60
Q

beta oxidation purpose and location

A

breakdown of fatty acyls to acetyl CoA to produce energy ( NADH , FADH2) . Acetyl CoA can enter the CAC to produce more energy
mitochondria

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61
Q

ketolysis produce and location

A

breakdown of ketone bodies to acetyl CoA Acetyl CoA can enter the CAC to produce more energy
mitochondria

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62
Q

Citric Acid Cycle purpose and location

A

breakdown of citrate (made from Acetyl CoA and oxaloacetate) to produce energy (NADH, FADH2 , ATP)
mitochondria

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63
Q

glycolysis aerobic versus anaerobic

A

aerobic - pyruvate enters CAC and undergoes oxidative phosphoralization leading to the net production of 32 ATP molecules

anaerobic - pyruvate converts to lactate through anaerobic glycolysis

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64
Q

why does conversion of pyruvate to acetyl Coa only happen under aerobic conditions

A

ATP is needed to convert pyruvate to acetyl CoA. without oxygen, no ATP can be made in oxidative phosphorilization

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65
Q

with a lack of oxygen, pyruvate converts to lactate rather than …. why?

A

Acetyl CoA, because it regenerates NAD+

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66
Q

what are the substrates in gluconeogenesis

A

mitochondria:
certain amino acids (make pyruvate and oxaloacetate)
cytosol:
lactate
glycerol

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67
Q

why does the liver release glucose?

A

to raise blood sugar levels when they are low

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68
Q

what is the energy input for glycogenesis?

A

anabolic process
ATP
- not recuperated via glycolysis
UTP
- P breaking off UTP, similar to ATP breaking off P

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69
Q

what does the pentose phosphate shunt make?

A

NADPH (used for fatty acid synthesis)
5 C sugars (such as ribose - 5- P for nucleotide synthesis

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70
Q

what energy is produced in beta oxidation?

A

NADH , FADH2

71
Q

in beta oxidation, what are the fats then broken down into? then what happens if we want more energy?

A

acetyl CoA, enters the CAC

72
Q

excess glucose can divert to make …

A

fatty acids

73
Q

if you dont need fatty acids for energy, how do you store them for later retrieval and use ?

A

triglycerides

74
Q

lipolysis releases fatty acids from …

A

triglycerides

75
Q

why are triglycerides useful for energy

A

compared to glycogen, TGs take up less space therefore they can store more energy

76
Q

the liver can make ketone bodies from … this is called …

A

acetyl CoA , ketogenesis

77
Q

ketone bodies are broken down to make …

A

acetyl CoA

78
Q

any cycle that can lead to the production of acetyl CoA can feed into … to ….

A

CAC , make more energy

79
Q

what three pathways feed into CAC

A

glycolysis, beta oxidation and amino acid metabolism

80
Q

the ETC is found in the

A

inner mitochondrial membrane

81
Q

The ETC takes electrons from … and … and passes then down the chain of electron carriers with …

A

NADH and FADH2, increasing affinty

82
Q

there are … ways that a N can be incorporated into an amino acid …. (indirect) … .. (indirect) and direct incorporation

A

transamination and transamidation

83
Q

transamination involves …. an …. group from a amino acid to an ….

A

transferring , amino , alpha ketoacid

84
Q

amino acid and alpha keto acid pairs

alanine and …..
glutamate and …..
aspartate and ….

A

pyruvate
alpha ketoglutarate
oxaloacetate

85
Q

transaminations require coenzyme …

A

pyridoxal phosphate PLP (vitamin B6 )

86
Q

transamidation is similar to transamination, except

A

the N comes from amido instead of amino

87
Q

direct amino acid anabolism is …

A

the addition of N directly from ammonia

88
Q

what three amino acids are in the glutamate family

A

glutamine(direct incorp) , proline and arginine( transamination)

89
Q

what 5 amino acids are in the aspartate family

A

asparagine(direct incorp) , lysine , methonine , theronine and isoleucine

incorporation of N via transamination

90
Q

what three amino acids are in the pyruvate family

A

alanine , valine and leucine

incorp of N via transamination

91
Q

what two amino acids are in the serine family

A

cysteine and glycine

incorp by transamination

92
Q

to be used as a coenzyme, folate first converts to …

A

THF

93
Q

folate enzymes assist in …

A

1-C transfers (transfers of methyl groups)
ex.
ser to glycine
making purines and pyrimidines

94
Q

what three amino acids are in the aromatic family

A

tryptophan , tyrosine and pheynlalanine

95
Q

phenylketouria (PKU) is a recessive disorder with a deficiency in ….. which cases a build up of … which is then converted to phenylketone and excreted in urine

A

phenylalanine hydroxlase

Phe

96
Q

what amino acid is in the histidine family

A

histamine

97
Q

PVT TIM HALL
what are the dietary essential amino acids?

A

pyr
Val
Tyr
T
Iso
Meth
Histine
Arg
Lysine
Leucine

98
Q

what are the two deamination pathways?

A

general - glutamine synthase reaction (extra hepatic to liver)

muscle to liver - glucose alanine cycle
- results in alanine carrying N to the liver to make
urea

99
Q

describe two ways for N to get from the extra hepatic tissues to the liver

A

amino acid transport
urea cycle

100
Q

describe the glucose alanine cycle

A

working muscles break down amino acids to release alanine, alanine gets released in the blood stream during high amounts of energy demand, the liver takes it up and converts it to glucose through gluconeogenesis providing a source for other tissues

101
Q

where does the urea cycle occur

A

liver

102
Q

the urea cycle is a combination of:….. and …. to make ….

A

ornithine and carbamoyl phosphate to make citulline

103
Q

through a series of reactions in the urea cycle the products are:

A

urea and ornithine (used to start the cycle over again)

104
Q

how many Ns does urea have? from where?

A

2, carbamoyl phosphate and aspartate

105
Q

where does carbamoyl phosphate come from?

A

C and O come from bicarbonate and the P comes from ATP, N comes from ammonia

106
Q

arginase is only found in the …

A

liver

107
Q

what is the cost of ATP to make urea

A

4, 2 ATP for each amino group

108
Q

urea connects to the CAC via

A

fumarate

109
Q

in the urea cycle, Asp donates a N and leaves as … which enters the CAC

A

fumerate

110
Q

oxaloacetate can undergo transamination to make ..

A

Asp

111
Q

once the amino acid group has been removed, the remaining C skeletons can be classified as: ……… and ……

A

Glucogenic
Ketogenic

112
Q

glycolysis can be divided into two main phases :

A

preparative phase and ATP genrating phase

113
Q

how many ATP are required in the prepatory phase of glycolysis?

A

2

114
Q

how many ATP are created during the generating phase of glycolysis

A

4

NET 2 gained

115
Q

how many NADH are generated per glucose molecule and where does it go?

A

2 and it goes to the ETC

116
Q

what are the three irreversible reactions of glycolysis

A

glucose -> glucose 6 phosphate
fructose 6 phosphate -> fructose 1,6 biphosphate

phosphenolpyruvate -> pyruvate

117
Q

gluconeogenesis occurs in the

A

liver and kidney

118
Q

gluconeogeneisis is especially important in …

A

fasting

119
Q

is gluconeogenesis simply a reverse of glycolysis?

A

no, there are irreversible steps

120
Q

lactate once in liver is converted back to

A

pyruvate

121
Q

what is the cori cycle

A

the conversion of lactate to glucose through glycolysis (pyruvate first) and glyconeogenesis between the muscle and liver transported through the blood

122
Q

glycerol can enter gluconeogensis pathway by converting to

A

DHAP

123
Q

glucogenic amino acids can enter gluconeogensis by …

A

being converted directly into pyruvate or into a citric acid cycle intermediate

124
Q

alanline can be converted to …. in the ..

A

pyruvate, mitochondria

125
Q

glucogenesis begins in the …

A

mitochondria

126
Q

lactate is converted into pyruvate in the …

A

cytosol, it is then immediately shuttled into the mitochondria

127
Q

once pyruvate is in the mitochondria it is then converted into …

A

oxaloacetate

128
Q

oxaloacetate can not cross into .. and therefore requires shuttle systems

A

the mitochondria

129
Q

Malate shuttle is used when starting substrate is

A

alanine

oxaloacetate is converted to malate

130
Q

lactate is converted to … in the cytosol …. then enters into the mitochondria and is converted into … , …. is then converted into phosphophenylpyruvate which is then shuttled into the mitochondria to continue with gluconeogenesis

A

pyruvate
pyruvate
oxaloacetate
oxaloacetate

131
Q

an acid is a molecule that can give up a

A

H+

HCl

132
Q

a base is a molecule that can give up an

A

OH-

NaOH, when added to water it completely ionized

133
Q

weak acid CH3COOH will ….. when added to water

A

partially ionize

134
Q

henderson hassleback equation is

A

pH = Pka + log (base / acid)

135
Q

weak acid will buffer … unit above or below the pKa

A

1

136
Q

the henderson hassleback equation calculates

A

pH of a solution given the pKa of a weak acid or base and the concentration of the protonated or deprotonated forms

137
Q

when salt and acid are equal what is the resulting pH

A

4.74

138
Q

what buffer is used in the extracellular fluid

A

bicarbonate - carbonic acid buffer

139
Q

what buffer is used in the RBC

A

Hb buffer system

140
Q

what buffer is used intracellularly

A

phosphate buffer

141
Q

protiens act as intracellular …….

A

plasma buffers

142
Q

the bicarbonate - carbonic acid buffer is in equilibrium with dissolved CO2 because

A

carbonic anhydrase action

143
Q

the bicarbonate carbonic buffer is the most effective

A

extracellular buffer

144
Q

why is bicarbonate buffer so effective?

A

carbonic andrahase rapidly catalyzes the formation of carbonic acid from water and carbon dioxide

carbonic acid (protonated) dissociates into bicarbonate (deprotonated) and H+

145
Q

what is important about carbon dioxide formation in the tissues

A

when Co2 is produced it will dissolve and be reconverted into carbonic acid (H2CO3) by carbonic anhydrase in the red blood cell . it will then ionize and be exported in the plasma via the HCO3 / Cl transporter

146
Q

when the red blood cell reaches the lungs HCO3 is transported back into the red blood cell , then is converted into .. and .. by …….. and the …… is released in the lungs

A

H2O and CO2
CO2

147
Q

why is carbonic andrahase so important?

A

because we could not get rid of CO2 without it

148
Q

what are the four major tissue types

A

nervous tissue, epithelial tissue , muscle tissue and connective tissue

149
Q

what is the matrix made out of in connective tissue

A

fibers (collagen, elastic fiber and reticular fibers) and ground substance (polysaccharide and protien complexes for most connective tissue

150
Q

what is responsible for the structural characteristics of connective tissue

A

fibers
- collagen
- elastic fibres (elasticity)

151
Q

what is ground substance in connective tissue

A

can be simple globular protiens
can be aggregates of protiens and large polysaccaharides
both are surrounded by water

152
Q

fibroblasts do what to the matrix

A

produce matrix

153
Q

macrophages do what in the matrix

A

immune cell for repair and defence

154
Q

adpocytes store

A

fat (triglycerides)

155
Q

enteric ganglia help regulate what?

A

activity of the gut

156
Q

microgalil (

A

clean up debris

157
Q

schwann cells

A

insulation

158
Q

astrocytes

A

support neurons

159
Q

oligodendrocytes

A

insulate axons

160
Q

metabolic organelle without a membrane

A

ribosome

161
Q

structural organelle without membrane

A

microfilaments
intermediate filamaments
microtubules
centrosomes

162
Q

rough ER is responsible for

A

protien synthesis , modification, trafficing

163
Q

smooth ER is responsible for

A

lipid synthesis , general metabolic functions, calcium physiology

164
Q

the golgi apparatus is

A

a site of protein modification and carb synthesis that works together with ER

protiens - formed by attaching carb to protein that have been transported from rER

165
Q

mitochondria is responsible for

A

redox reactions that drive the phosphorlization of ADP and ATP
- heme production
- urea cycle
- calcium homeostasis

166
Q

vesicles have ….. functions and vacuoles have ….. functions

A

transport, storage

167
Q

ribosome is an organelle ……… that uses mRNA to accomplish

A

without membrane , protien translation

168
Q

whats the difference of free ribosomes verus ribosomes attached to rER

A

free - translation of cytosolic proteins
rER - translation of protiens that will be modified and transported in ER

169
Q

actin filaments are responsible for ….

A

shape of the microvilli

170
Q

desmin is organised to

A

provide strength across the cell

171
Q

a very large number of tiny vessels

A

capillaries

172
Q

large capacity vessles

A

venules and veins

173
Q

stroke volume x heart rate = ?

A

flow (cardiac output)

174
Q

what are the major baroreceptors

A

carotoid arteries
arch of the aorta

175
Q

gas and pH sensors are found in …

A

the same location as baroreceptors
carotoid arteries
arch of the aorta

176
Q

cerebral cortex respiratory role

A

voluntary control

177
Q

hypothalamus respiratory role

A

regulates breathing on emotional states, pain, body temp

178
Q

proprioceptors respiratory role

A

muscles and joints move, sends signals to brain stem - ventillation changes in inticipation of increased MSK o2 or co2 needs

179
Q

chemoreceptors respiratory role

A

increase ventilation when arterial oxygen drops amd carbon dioxide increases

180
Q

medulla and pons respiratory role

A

regulate activity of major muscles for ventillation

Biomed (9 decks)

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